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Samus Aran was originally a native of the Earth colony K-2L, where she lived with her parents Rodney and Virginia Aran. At the age of three, the colony was visited by the Chozo, who hoped to obtain some of the Afloraltite that the colony mined there. During this visit, Samus caught the attention of Old Bird, one of the Chozo elders. The two of them went for a walk where they began to strike up a friendship. Samus began to call him “Grandpa” and Old Bird introduced her to Pyonchi, a Rabbilis whom she adopted as a pet.

However, a Space Pirate raid led by Ridley soon commenced on the colony. Finding herself face-to-face with Ridley himself, the naive Samus asked him if they could become friends. In response, Ridley attempted to kill Samus, but her mother pushed her daughter out of the way at the cost of her own life. Meanwhile, Samus' father sacrificed himself to destroy Ridley’s flagship. Little did Ridley know that, in killing Samus’ mother and attempting to kill Samus, he succeeded in creating his greatest enemy.

A young Samus during the attack on K-2L.

Now orphaned, Samus was the sole survivor of the attack on K-2L. Eventually, the same group of Chozo found her alone and stranded on the destroyed colony and Old Bird decided to take custody of Samus. The Chozo brought her to their planet, Zebes and raised her. In order to survive the planet's harsh conditions, Samus was infused with Chozo DNA[1], and later gifted an advanced Chozo Power Suit.

Samus trained under the Chozo for many years, and had surpassed the physical limits of ordinary humans by 14. The Chozo were initially unsure if she was able to become a true warrior until they witnessed her compassion for a flock of Iono Feria that went insane as a result of exposure to Badger Clover. After Old Bird told Samus that she had his confidence, she left the planet for the Federation.

Enrolling in the Federation Police, Samus excelled in the academy, and was promoted to the Star-Trackers, an elite force that only one in a million police officers was qualified for. Under Chief Hardy, one of her early assignments was to the human planet Jigrad, which the Space Pirates had recently enslaved. When the pirates threatened to execute a child slave named Damara simply for being unfit for work, Samus and her squadmates Kreatz and Mauk attacked without orders. This led to the first Federation imprisonment and interrogation of a Space Pirate - a matter which also involved a military leader named Adam Malkovich, leading to his introduction to Samus. The interrogation revealed that the Space Pirate’s actions on Jigrad were just a distraction from their invasion of Zebes. Hardy ordered Samus to wait for the Army to be deployed, but Samus and her teammates disobeyed and traveled to Zebes to aid the Chozo. After a run-in with Adam, she was told that she was given 48 hours before the army arrived.

Samus, Kreatz and Mauk arrived at Zebes and learned the Space Pirates were hoping to gain the whole of Chozo knowledge. The Chozo either fled or surrendered and the first Metroid was rogue in the base. Samus discovered that Mother Brain and the Chozo Gray Voice established a "satisfactory cooperative relationship" with the Pirates, in which Mother Brain would be their new leader and use them to reunite the galaxy. Mother Brain offered Samus the role of "master" of the Space Pirates - an offer that Aran quickly refused. At this time, Ridley arrived and taunted Samus over the death of her parents. All of this triggered Samus' posttraumatic stress disorder due to the repressed memories of the K-2L attack. Samus was later saved by her squadmates causing a distant distraction and the newly rescued Chozo helped Samus get over her posttraumatic stress. Samus donned her Power Suit and defended the party from Ridley, who then retreated to defend Mother Brain from an attack by Gray Voice, who had revealed his true allegiance and was attacking Mother Brain. Learning about Gray Voice’s plight from the rescued Chozo Platinum Chest, Samus wanted to assist, but decided to help the evacuation. While escaping, Samus somehow felt Gray Voice's final moments due to their shared DNA and heard his final words telepathically. Stating that she had become strong, the dying Chozo asked that Samus use her power to help protect the beings in the galaxy who needed it.

After the infiltration of Zebes, Samus (Between 15–17 years old) worked on the VIXIV under General Adam Malkovich. Here, she met Anthony Higgs and Adam's younger brother, Ian Malkovich. It remains unknown how long she served with Adam’s unit, but long enough to develop a strong relationship with Anthony, Ian and Adam. Adam would always finish his orders with the question, "Any objections, Lady?" as a way of cementing the trust between the two of them. Samus felt like Adam was the only person who truly understood her, and grew to view him as her best friend and surrogate father figure. However, Samus would leave the VIXIV after the death of Ian, whom Adam sacrificed to save 300 innocents on the Lusitania.

Samus vanished completely, abandoning her post in the GF Police. In Metroid: Other M, she stated that her reason for doing so was that she was still young and relatively inexperienced at the time. Samus did not resurface until a few years later. By this time, she became universally renowned as a Bounty Hunter by singlehandedly hunting down numerous Space Pirates, including stopping an assassination attempt at the inauguration of Chairman Keaton. So much of her life during this time was shrouded in mystery that the public believed her to be a male cyborg, not the same woman who graduated first in her class at the GF Police.

Now a renowned Bounty Hunter, Samus was summoned by the Galactic Federation. Previously, a Federation Planet Reclamation Division had been sent to capture Metroid specimens for study, but the Space Pirates had swept in, killed the crew, and stolen the Metroids. The capture of this creature was a disastrous blow to the Federation. With hundreds of Metroids under their power, the Space Pirates would inevitably begin a campaign to conquer the rest of the universe. Galactic Civilization would end.

After a long and harrowing search, the Federation Police tracked the Pirates to Zebes. They launched an invasion, but Pirate resistance was too strong. After much debate, the Federation decided to turn to Samus to infiltrate the base at Zebes. She was given two objectives:

Samus arrived on Zebes and soon discovered that in order to access the central Space Pirate base in Tourian, she had to kill the two Pirate leaders situated on the planet: her old foe, Ridley, and his partner Kraid. After discovering various Chozo artifacts located in multiple locations on the planet that served as upgrades for her suit, Samus was finally able to access the lower depths of Brinstar, where she discovered Kraid waiting for her. A fierce battle ensued, which ended in Kraid's defeat. Samus then headed into the deep volcanic regions of Zebes, where she had several surprising encounters with Imagos, gigantic insects that grew from enormous grub-like larvae. When Samus arrived at Ridley’s lair, she soon encountered the Pirate leader, who had just arrived moments earlier after being sent to inspect the planet. The two faced off, with Samus intent on finally avenging her parents’ death. The bounty hunter emerging the victor. However, unbeknownst to Samus, Ridley did not die from his crippling wounds.

After defeating Kraid and Ridley, Samus was granted access to Tourian, where she discovered that the Space Pirates had apparently underestimated the Metroids’ intelligence. A massive breakout had occurred, and all Pirate personnel present at the time of the breakout were dead. Mother Brain herself, however, was protected by her Chozo-built facility and so completely unharmed. As a result, Metroid cloning had proceeded as though nothing happened, so the Metroid population had risen to an astonishing level. Samus engaged the Metroids she encountered but found that they were impervious to most of her weaponry. Only by exploiting their weakness to cold with the Ice Beam could Samus hope to overcome them.

Samus soon arrived at Mother Brain’s chamber and fought her way past the defense systems. The two engaged in an arduous duel, but Mother Brain was ultimately defeated. Unfortunately for Samus, Mother Brain's death activated a hidden fail-safe that began a countdown for the self-destruction of the entire Pirate base. Samus barely managed to make it out to her gunship in time.

Unfortunately, escape was not as easy as Samus had expected. As soon she left the atmosphere, Space Pirate vessels ambushed her; during the ensuing chase, Samus was shot down, and her ship crash-landed back on Zebes. Samus survived, but the explosion had destroyed her Power Suit. The only weapon left available to her was a mostly-useless stun pistol. Her only option was to sneak inside the Space Pirate Mother Ship, which had landed in a nearby valley, in hopes of hijacking a ship and escaping. The next morning, Samus climbed in through the air ducts and began her infiltration. She privately admitted that sneaking in to a highly armed area like the Mother Ship, especially while she was in her Zero Suit, was not the wisest strategy, but knew that she had no other options but to do so. Unfortunately, her plans were quickly botched when she was spotted by several Pirates, who quickly set off alarms throughout the entire ship. Though she managed to outwit them many times, Samus was ultimately forced to retreat to the nearby ruins of Chozodia.

In the ruins, Samus discovered a sacred Ruins Test which she had visited once as a young child. Upon her discovery, the Test activated; Samus had to face a mirror image of herself along with powerful bolts of lightning hurled by the hieroglyphic. Ultimately, Samus succeeded in passing the test, and the statue rewarded her with the Legendary Power Suit, and unlocked the three Unknown Items she had previously acquired: the Plasma Beam, the Gravity Suit, and the Space Jump. Now more powerful than ever before, Samus stormed the Pirate Mothership, leaving many dead Pirates in her wake.

Eventually, Samus made it to the bridge of the Mothership where she discovered the Ridley Robot, a gigantic robot built in Ridley’s likeness. The robot engaged her in a fierce battle, but Samus was easily able to destroy it. As it shut down, it activated the self-destruct for the Pirate Mothership. Samus raced through the corridors of the Mothership, battling numerous Pirates along the way, until she managed to hijack a Space Pirate Escape Ship. Samus quickly flew out of the ship and left Zebes as the Pirate Mothership exploded behind her. Samus had fulfilled her Zero Mission.

Three years later, Samus’s next mission led her to another planet in the Zebesian system: Tallon IV. She intercepted a distress signal sent from the Space Pirate frigate Orpheon and immediately flew in to investigate. Once inside, she found dead and dying pirates everywhere while vermin ran amok in the ship. It did not take Samus long to discover the source: a Parasite Queen the Pirates had been performing experiments on had broken out and stationed itself in the Frigate’s Nuclear reactor core. Samus killed the creature, but the dying beast slipped into the reactor, causing a malfunction that threatened to destroy the entire vessel. Samus ran for her life through the ventilation tunnels, but to her great surprise, she found herself reunited with Ridley, who had been given many cybernetic implants and been transformed into a powerful cyborg. Samus chased him through the ship, but along the way, an explosion rammed her into a wall, causing her Power Suit to malfunction. This caused most of her abilities to go offline, leaving only the Arm Cannon functional. Samus quickly left the dying frigate and chased Meta Ridley in her gunship, but he proved faster than expected and soon disappeared from her radar. Samus was forced to track him on foot, and so, even in her weakened state, she chose to land on the planet below: Tallon IV.

After traversing the jungles in the Tallon Overworld, Samus discovered an elevator which led to some deserted Chozo Ruins. There, she discovered that 50 years previously, a colony of Chozo had come to the planet to regain their spirituality. Unfortunately, a mysterious meteor eventually struck the planet, bringing with it a Great Poison and The Worm. The Great Poison quickly began spreading across the planet, killing most life in its path and corrupting the rest into savage mutants. Many of the Chozo were driven insane and became menacing spirits; the few survivors fled to an unknown location. The remaining sane Chozo on Tallon IV, now reduced to mere ghosts, managed to seal off the Impact Crater within a seal called The Cipher, locking up The Worm and most of the Great Poison with it. The Space Pirates fleeing the destruction of the base at Zebes had then landed on the planet; they began mining the Great Poison (which they named Phazon) after discovering it could be used to enhance the fighting potential of various creatures, including themselves.

Samus journeyed through Tallon IV, regaining her lost weaponry and collecting sacred Chozo Artifacts, learning along the way that the Chozo had prophesied that she was the one destined to destroy the Worm and the Phazon there. She also swept through the Phazon Mines the Pirates had set up, destroying the Phazon-infused experiments she found there. Samus eventually confronted the most powerful of these mutated Space Pirates: the Omega Pirate. After a challenging battle, Samus managed to defeat the beast, but in its death throes, it fell on Samus and melted into pure Phazon. The viral radiation dramatically altered her Power Suit, turning it into the Phazon Suit; fortunately, this corruption proved beneficial as it allowed her to safely come in contact with and harness the power of Phazon.

Having collected all the Chozo artifacts and suit upgrades, Samus returned to the Artifact Temple and activated the Cipher in preparation for entering the Impact Crater. Just before the statue's seal deactivated, however, Meta Ridley flew in and destroyed the statue. He then attempted to kill Samus, but Samus managed to burn off his wings then overload his life-support. Just as Meta Ridley was brought to death’s door again, the Temple's Chozo statues there fired powerful lasers at his chest, blasting him off of the edge into the abyss. The Chozo Ghosts within the statues then undid the seal themselves, allowing Samus into the Impact Crater. Inside, Samus discovered the sleeping Metroid Prime, the source of all Phazon on the planet. Samus managed to destroy its armor, forcing the creature to reveal its true form. Unable to damage it further with conventional weaponry, Samus was forced to overload it by harnessing pure Phazon via her Phazon Suit. The Metroid Prime began to die, but in a last-ditch attempt to save itself, it shot out a tentacle and absorbed Samus’s Phazon Suit before exploding. Samus ran for her life as the entire Impact Crater burst into flames. Though Tallon IV had been cleansed of Phazon, The Worm was not yet dead and would soon be reborn as Dark Samus.

Some time afterward, a mysterious telepathic message was sent out from the Tetra Galaxy saying, "The secret to ultimate power resides in the Alimbic Cluster." Samus was sent by the Federation in order to determine the truth about this message. Unfortunately, the message had also been received by other parties and soon many other hunters began heading to the Alimbic Cluster, each with their own motives for seeking the "ultimate power". To gain it, one had to find the eight Octoliths which would power the Alimbic Cannon, allowing access to a structure in another dimension called the Oubliette. The Octoliths were all under guard by robotic beings: the Cretaphids and the Slenches.

Between skirmishes with these beings and the other hunters, Samus discovered that the Alimbics, the former inhabitants of the Alimbic Cluster, had been experiencing a time of peace and prosperity until a monstrous being named Gorea had arrived in the form of a comet and began wreaking havoc upon their civilization. The Alimbics were forced to sacrifice themselves to seal away Gorea within the Seal Sphere, which was kept in the Oubliette. They also left a cryptic prophecy on how one might defeat Gorea.

Gorea.

After collecting all eight Octoliths and using them to activate the Alimbic Cannon, Samus and the other hunters raced to the now-accessible Oubliette. The other hunters got there first, and inside discovered an immobile structure. They began firing at it, mistakenly believing it to hold the ultimate power. To their surprise, Gorea instead emerged from the broken structure. Samus arrived just in time to see Gorea shoot out massive tentacles and drain the other hunters of their powers. The defeated hunters disappeared, and Samus alone remained to fight Gorea. She first activated the panels around the arena in accordance with the Alimbic prophecy, then began battling Gorea by exploiting its link to the Seal Sphere. Gorea then revealed its final form and continued its assault. Fortunately, Samus gained access to the Omega Cannon, which allowed her to defeat Gorea's second form. Gorea and the Oubliette exploded, while Samus and the other hunters escaped with only their lives. Once she was back in the safety of space, Samus received a vision where three Alimbic spirits appeared to thank her.

Samus was soon given yet another assignment from the Galactic Federation; this time, she was asked to track down a missing brigade of Federation Marines, GFMC Task Force Herakles. Samus headed to the planet Aether located in the Dasha region of space, where the troopers’ distress signal was coming from. Samus attempted to land on Aether, but her gunship was caught in the dimensional storms raging on the planet and was badly damaged. Luckily, her ship landed not far away from the troopers’ makeshift base. Upon entering it, however, she found she was too late: All of the troopers had died in an attack by unknown assailants. Before she could discover the source, many of the dead troopers reanimated and began firing at her.

Samus fled the base, with the undead troopers in pursuit, but once she was safely outside, she encountered something even stranger: A mysterious black and blue being wearing a suit similar to hers was entering a mysterious portal to an unknown location. Samus followed the being into the portal, only to find herself in a nightmarish replica of the room she had been in, where her dark twin was absorbing a large quantity of Phazon. The being then destroyed a crystal near Samus, which was generating a force field protecting the hunter from the region's poisonous atmosphere. The double then departed, leaving a vulnerable Samus to the clutches of savage creatures that quickly surrounded and overwhelmed her. Samus was forced to retreat back through the portal, only to learn that the dark creatures had robbed her of many of her suit upgrades.

Samus made her way through the catacombs of Aether until she discovered the source of the distress signal: the Federation troopers' damaged ship, the GFS Tyr. Accessing the ship’s log, she discovered that the Task Force had been stranded on Aether when their ship was damaged in pursuit of a downed Space Pirate frigate. Eventually, they were all killed after repeated assaults by Dark Splinters, though one of the troopers managed to send the distress signal before his death.

The Temple Grounds.

Samus’s ship was still repairing itself, so she went on a search to identify the cause of the attack and recover her stolen weaponry. She began finding signs of an intelligent civilization living on Aether and chose to investigate. Her search eventually led to the Great Temple, where she found dozens of beings suspended in cryogenic hibernation. Before she could investigate further, she was immediately attacked by an Alpha Splinter, which was almost immediately possessed and transformed into a Dark Alpha Splinter. Samus managed to kill it, but a strange glowing object emerged from the dead insect and entered her suit.

Samus continued exploring the building until she encountered a being known as U-Mos, the Sentinel of the Luminoth. U-Mos informed her that his species, the Luminoth, had migrated to the planet after being drawn by its unique energy. They had lived in peace until a meteor much like the one that impacted Tallon IV impacted the planet, straining the planet’s fragile dimensional stability and tearing it between two different dimensions in spacetime: the original Aether and a twisted, corrupted version called Dark Aether, which was home to a malevolent race called the Ing; it was the Ing who were responsible for the deaths and possession of the troopers, as well as the theft of Samus' upgrades. The Luminoth had been involved in a long war with the Ing for the Light of Aether and were at the verge of defeat when Samus had arrived. U-Mos also revealed that, after her battle with the Dark Alpha Splinter, Samus had recovered the Energy Transfer Module that had been stolen by the Ing years earlier. Now that she had it, she could transfer the planet's energy from Dark Aether to Light Aether; without it, the shadowy replica would collapse forever. Samus agreed to seek out the Energy Controllers to restore the Light of Aether to the Luminoth.

Samus’ mission took her all through Aether and Dark Aether, where she faced many Ing attempting to kill her for assisting the Luminoth, as well as several skirmishes with her mysterious double, who was dubbed "Dark Samus". She also reclaimed her stolen weaponry from the various Ing Guardians who had made use of it, and obtained Luminoth upgrades such as the Dark Suit. Once she had restored the three energy controllers to transfer the Light of Aether, U-Mos thanked her with the Light Suit, a suit that contained the Light of Aether within itself. Then, he told her of her most dangerous task: to reach the final Energy Controller, hidden within the Sky Temple. To enter the Sky Temple, though, she had to find the nine Sky Temple keys scattered about Dark Aether.

Samus faces the Emperor.

Within the Sky Temple, Samus faced the Emperor Ing, a mighty behemoth that ruled the entire Ing race. Although she was almost defeated, Samus prevailed, killed the Emperor, and obtained the last of the planetary energy. Without the energy, Dark Aether started to fall apart, leaving her with only minutes to escape. Samus raced down to the Sky Temple gateway, but before she could flee the crumbling dimension, Dark Samus confronted her once more. The two dueled to the death, but Samus took advantage of her foe's sole weakness — an overload of Phazon — and defeated her doppelganger once again. In her weakened state, Dark Samus attempted to steal Samus’ Light Suit, but instead dissipated into thin air. Samus then entered the portal, leaving Dark Aether to collapse behind her. The Luminoth, who had just returned from their cryogenic sleep, rejoiced and thanked Samus for freeing them from the Ing. Samus then gave them back the equipment she had borrowed from them, returned to her gunship, and she flew off into the vast darkness of space.

Six months later, Samus was summoned to the battleship G.F.S. Olympus in orbit with the rest of the Federation fleet above the planet Norion in the Kalandor region, where she would receive her instructions for her next assignment. On the way over, however, she experienced a nightmare of Dark Samus' resurrection, as well as an anomaly within her cryostasis (which is heavily implied to have been caused by Dark Samus itself). On board the Olympus, she met with Fleet Admiral Castor Dane and Aurora Unit 242, along with fellow bounty hunters Rundas, Gandrayda, and Ghor. Dane and 242 informed of their mission:to deliver a vaccine to the Aurora Units in that system, who were suffering from a Space Pirate-engineered virus. Just as the mission briefing ended, the Pirates launched a surprise attack; all the bounty hunters, including Samus, headed down to their ships to assist with the battle at Norion’s main base, fighting any Pirates they encountered in the corridors. Upon landing there, Samus was informed the Space Pirates had disabled the generators to Norion’s planetary cannon; thus, she and the other hunters were given the responsibility of restoring them while the Federation Marines held off the invading Pirate forces.

Samus at the time of Metroid Prime 3.

Samus and the other hunters raced through the base, turning on each generator they found to restore power to the cannon. The situation soon became dire when the Federation discovered why the Pirates were attacking: a massive Leviathan was headed on a collision course with Norion. The invasion was intended to stall the Federation fleet until the Leviathan could arrive and crash into the planet, spreading Phazon everywhere. Samus headed to the final generator, only to find her old nemesis Meta Ridley waiting for her. In the ensuing melee, Meta Ridley broke through the floor and the two of them hurtled down the 1600-meter shaft, dueling all the way. Just as Samus finished off Meta Ridley, Rundas came down to rescue her and the two flew out of the shaft together. Samus restored the final generator and she and the other hunters rushed straight to the control tower to activate the cannon. As soon they made it to the top, though, they encountered Dark Samus, who had indeed been resurrected by consuming the Pirates' Phazon supply. After a brief struggle, Dark Samus incapacitated all four of them with a massive burst of Phazon, then flew off. Though barely conscious, Samus managed to fire the cannon just before she fainted, destroying the incoming Seed and saving Norion.

Samus awakens after a month of being comatose.

One month later, Samus awoke to discover that she and her fellow hunters’ bodies were self-producing Phazon, with no negative side effects to their health. The Federation medics working on her had therefore equipped her with a Phazon Enhancement Device. Through this suit, she could harness her own Phazon to enter Hypermode, a function that would allow her to energize her suit and weapon systems with Phazon and giving her access to devastating powers. Samus was then informed by the Aurora Unit 242 that her fellow hunters had awoken two weeks before she had. They had also been given PEDs and were dispatched to the planets Bryyo, Elysia, and the Pirate Homeworld, which had also been struck by Leviathans. Unfortunately, the Federation had lost contact with all of them one week later. Samus was then tasked with completing the missing hunters’ missions to destroy each Leviathan, as well as finding out exactly what caused the Federation to lose contact with them.

Samus first traveled to the planet Bryyo, where Rundas had been assigned, and learned that the Leviathan infecting the planet was protected by two shield generators. Samus obtained the locations of the generators from a downed Federation ship, the G.F.S. Theseus. After leaving the ship, though, she noticed Rundas watching her from a distant cliff. Travelling to Bryyo's eastern region to destroy the first generator, she discovered Rundas' ship had already landed before her.

Along the way to the generator, Samus learned that her internal Phazon - once thought to be benign - could cause her body to overload with Phazon - meaning that every use of Hypermode put her at risk of being completely corrupted by the Phazon. Soon after, she encountered Rundas himself, and made to greet him; however, his uncharacteristic silence gave her pause, and he left her without a word. Shortly afterward, he saved Samus from waves of Pirates, but then attacked her as well; Samus realized that her comrade had succumbed to his own corruption, and was now a slave to Dark Samus' will. Reluctantly, she was forced to fight her former friend in a grueling duel, ultimately defeating him. But as she approached Rundas, spikes of ice erupted from the ground, impaling Rundas and killing him instantly. To Samus' shock, the specter of Dark Samus then materialized, and absorbed Rundas' body before Samus could intervene.

Following Rundas' death, she then proceeded to destroy the two generators, leaving Bryyo's seed exposed. Flying directly into the bowels of the Leviathan, she destroyed the corrupted Mogenar war golem within, which released a massive wave of Phazon that caused Samus' own internal corruption to spread. Nevertheless, she proceeded to destroy the Leviathan's core, saving Bryyo from further corruption.

After being briefed by Unit 242, Aran proceeded to the planet Elysia, which was home to Skytown, an ancient, floating Chozo facility where Ghor had been assigned. Fighting past SkyTown's corrupted robotic inhabitants, Samus found her way to SkyTown's Aurora Unit 217, to whom she successfully administered the vaccine. However, the now-corrupted Ghor intervened, using his Plasma Cannon to sever 217's connections to the AU network. Shortly afterward, she discovered Ghor attempting to sabotage her Gunship, and was forced to fight him. After Ghor's defeat, the spectral form of Dark Samus again arrived to absorb him; Samus tried to save her fallen hunter, but could ultimately do nothing but angrily clench her fist. After fixing the damaged AU network, Samus was informed that the Federation had located the GFS Valhalla, and was asked to investigate. Upon arrival, she found it a desolate ghost ship, filled with corpses and Phazon-mutated creatures. After an initial investigation, she returned to Elysia, and the Aurora Units informed her of a plan they devised to bypass the shield protecting Elysia's Leviathan: Gather three components to a Theronian Bomb, which would then be dropped into the seed's shield. Unfortunately, this meant that Samus also had to be on board the bomb to defend it from Pirate forces, and flee before impact in an Emergency Evacuation Pod. After the shield was breached, Samus again destroyed the Leviathan's guardian - this time a corrupted robot known as Helios - and then the Leviathan itself.

With Elysia saved, 242 then informed Samus that the Federation had received an Emergency GF communication capsule from Gandrayda revealing the location of the Pirate Homeworld. On the planet, Samus learned that much of the planet was rendered inaccessible by deadly Acid Rain, but received a communication from an escaped Federation Trooper NZG41, who claimed he knew how to bypass the rain. Samus saved the trooper, but soon discovered that "NZG41" was actually a disguised Gandrayda, who was now fully corrupted. Samus fought the final hunter in all of her various forms in a vicious battle, but ultimately the shapeshifter fell. Like Rundas and Ghor before her, the screaming Gandrayda was absorbed by Dark Samus, but this time Samus grimly accepted the fact that there was nothing she could do, looking away as Gandrayda died.

After the battle and further investigation of the Pirate Homeworld, Samus disabled its planetary shield, allowing the Federation’s fleet to launch a full-scale assault on the planet. Samus personally led a team of Demolition Troopers to destroy the security door of the cargo line leading to the Homeworld's Seed. There, she encountered and defeated her old nemesis once again, now reborn as Omega Ridley. All of the Leviathans had been destroyed, but Samus had been corrupted to the point that she was now literally glowing with Phazon.

Afterward, she returned to the Valhalla to investigate its depths, and discovered that the Pirates had ignored most otherwise-valuable equipment, taking only one thing: The vessel's Aurora Unit, 313. In addition, she found the codes required to access the Pirates' Leviathan Battleship.

With this, Samus and the Federation were able to launch a final battle to destroy the newly discovered planet Phaaze - the source of all Phazon and Dark Samus' place of origin. Traveling with the Federation via a wormhole created by the Leviathan Battleship, Samus descended to the planet while the Federation kept the Pirate forces busy. As soon she set foot on Phaaze, Samus absorbed dangerous amounts of Phazon and was nearly corrupted completely; even after venting all her available energy tanks and locking herself in permanent Hypermode, she was living on precious borrowed time. Venturing to the planet's inner sanctum, she encountered Dark Samus, and, after a long battle, Dark Samus merged with the stolen Aurora Unit 313 that was linked with Phaaze's core. After one final battle, Samus was able to overpower and destroy both her doppelganger and the Aurora Unit. Since the Aurora Unit was linked to the planet's core, its destruction caused a chain reaction that resulted in the destruction of Phaaze and the erasure of all Phazon from the universe, including the Phazon inside Samus' body. The Federation fleet escaped via another wormhole, but lost contact with Samus in the process. Just as the Federation had given up all hope of Samus' survival, she flew in and reported that the mission had been completed, closing the curtain on the Phazon saga.

Samus reflects at Elysia.

After leaving the celebrating Federation fleet, Samus returned to Elysia, where she mourned the loss of her fellow bounty hunters on this mission. Eventually, she left Elysia and headed off to find her next mission, but failed to notice a mysterious gunship following her.

After a Space Pirate presence was discovered by the Galactic Federation in the Bermuda System, Samus was called in to investigate. The Bermuda System is a three-planet solar system with abandoned Galactic Federation facilities. The Federation Force, a team of highly trained soldiers wearing Mech suits modeled after Samus's Power Suit, was already there. Samus worked alongside them to battle Space Pirates, saving the group from a Rohkor Beetle at one point, but mostly gathering intelligence for them.

At some point, she was taken hostage by the Pirates and somehow put under mind control. When the Force boarded the Doomseye, a large Space Pirate battle station, the Pirates used technology from the ancient Bion race to increase Samus's size and forced her to fight the Federation soldiers. The Federation Force bested her and she was seemingly crushed by falling debris. The blow freed her from mind control, however, and after recovering, she saved the Force twice, first by destroying a group of Elite Pirates, and then by catching the soldiers with her ship when they were sucked into space. Samus told the Force that meeting them had been an honor, and then thanked them for saving her and the universe.

What happened after this period of time is unknown. However, ultimately the Galactic Federation decided that the Metroids were too dangerous to exist, given the devastation they had caused in Pirate hands. After two failed attempts by their own troops, the Federation asked Samus to exterminate them herself, given her long experience in dealing with the creatures.

Arriving on SR388, Samus learned that the planet's environment caused Metroids to mutate into different forms, each stronger than the last. She also discovered ancient Chozo ruins, including a golden seal that was tied to the corrosive purple liquid blocking access to deeper areas of the planet; every time Samus managed to successfully kill all the Metroids in an area, the seal would lower the liquid levels, allowing the hunter access to deeper levels where stronger Metroids were hiding. Her search finally led her to the Queen Metroid, which was responsible for the reproduction of the entire Metroid species. Samus managed to kill the beast and thus believed herself to have successfully eliminated the Metroids for good. As she continued down the tunnels, however, she found a single Metroid egg. As she stared at it, an infant Metroid hatched out of the egg and, upon seeing Samus, imprinted on her as its mother. Samus felt compassion for the infant and, going against her orders, took the Metroid Hatchling to her gunship and made preparations to leave the planet.

Before she could actually leave the planet with the infant, however, an unexpected threat arrived and grabbed the Metroid: her old foe, Ridley. Samus fought him over the baby, eventually grabbing his tail as he was flying away and proceeded to blast him directly in the exposed abdomen at point blank range until he was forced to let go of the baby Metroid before promptly blasting him in the wing and sending him flying into a cliff. However, Ridley rose from the rubble and resumed his attack on Samus, eventually blocking her attacks and throwing her against a wall before pinning her down to blast fire at her. She was saved by the baby, who proceeded to absorb enough energy from Ridley to rejuvenate her, allowing her to triumph over the Space Pirate leader. Afterwards, she then left the planet with baby.

Samus, knowing how valuable the Metroid hatchling could be to the Federation, headed to the Ceres Space Colony, and chose to turn it over to the scientists there, who believed they could harness the infant’s power for the good of mankind. Confident in their findings, Samus proceeded to leave the station. However, she had not even left the asteroid belt where Ceres was stationed before she received a distress signal from the scientists. Returning to Ceres, she discovered that the Space Pirates had attacked the station in hopes of stealing the Metroid. Ridley himself had captured the infant and was about to make off when Samus arrived. After a brief struggle, Ridley flew out of the station and set the self-destruct to destroy the entire station. Samus barely made it out alive, flying away in her gunship while Ceres exploded behind her.

Samus chases Ridley back to Zebes.

She managed to track Ridley and the other Pirates to Zebes, discovering that the Space Pirates had rebuilt their old base on the planet and had returned to their old plan of cloning Metroids. Mother Brain had returned as the head of the base, as had Ridley and Kraid. Two new Pirate generals had been recruited as well: Phantoon, a ghostly being that haunted the Wrecked Ship, and Draygon, a massive Evir which presided over Maridia. After defeating them all, Samus was granted access to Tourian. She proceeded to exterminate the Pirate-cloned Metroids she found there, but was suddenly attacked by a massive Metroid, far larger than any she had ever seen. All her weaponry was useless against it, and soon the Metroid had drained her suit to critical levels. Just moments away from her death, the Metroid relinquished its hold and fled after figuring out that it was Samus, leadin Samus to realize that it was the Baby, enhanced through unknown means.

Samus and Mother Brain duel at Tourian.

Samus continued through Tourian until she encountered Mother Brain and proceeded to destroy her tank as before. Though she appeared to be defeated, Mother Brain suddenly emerged from the wreckage in a massive new body. Samus fought with all her might, but Mother Brain retaliated with the Laser Brain Attack, leaving Samus near death once more. Just before Mother Brain could launch another blow, the infant Metroid suddenly arrived, sucked the life out of Mother Brain, then began transferring the life to Samus. Mother Brain was not yet dead, though, and it began attacking the Metroid. An energy shot from Mother Brain finished off the Baby, but Samus had been revived and used Mother Brain’s own Hyper Beam against her until she was no more. Mother Brain's death triggered yet another self-destruct mechanism, only this time, the entire planet was engulfed in the explosion. Samus escaped with her life, while Zebes, the ancient home of the Chozo and her childhood home, was lost forever.

Although she managed to escape from Zebes, Samus was injured from her fight against Mother Brain and from the mission overall, eventually resulting into her admission into a hospital. Samus recovered and flew off, but she still mourned the loss of the Baby. After several weeks of drifting aimlessly, Samus received a "Baby's Cry"-type distress signal directing her TO a facility known as the BOTTLE SHIP. She found that a Federation vessel had also received the S.O.S. and had docked on the BOTTLE SHIP. The crew of the ship, to her surprise, was the Federation squad she had been a part of when she had been enrolled in the GF Army, the 07th Platoon, consisting of several soldiers, namely Anthony Higgs and Adam Malkovich. She and the team were forced to cooperate in order to overcome the apparent dangers of the BOTTLE SHIP; Samus was allowed back onto the team provided that she followed Adam's orders. After restoring power to the Main Sector and being sent to inspect the Biosphere, Samus came across a small, furry creature that stopped to stare at her.

Samus battles multiple enemies in the depths of the BOTTLE SHIP.

After much discovery and exploration, Samus arrived at the Exam Center toward the rear of the Biosphere. There, she met up with her comrades and activated a computer terminal. The data revealed that the BOTTLE SHIP was a research station where bioweapons were being bred under the directions of Madeline Bergman. Noticing a large lizard-like creature attacking the soldiers outside, Samus raced to help them, but was ambushed and almost killed before Anthony shot it off of her, said creature fleeing immediately afterward. They then found the body of Lyle Smithsonian, who appeared to have been mauled by the creature. Samus also found the lifeless shell of the small white creature she saw earlier, which was actually the immature form of the lizard beast that had attacked her. Samus pursued the creature into the Pyrosphere but was soon ordered to go to the Cryosphere to search for survivors. There, she found the body of Maurice Favreau and noticed a young woman staring at her. From events that had taken place, Samus deduced that there was a traitor in the platoon and nicknamed him The Deleter. Returning to the Pyrosphere, she then discovered the beast she was tracking was actually her nemesis, Ridley. He hurled Samus' old friend Anthony into a pool of Lava, angering Samus and empowering her enough to defeat Ridley once again, though he managed to escape.

Samus and Adam are separated forever.

Entering the Bioweapon Research Center while tracking the Deleter, Samus once again encountered the young woman, who identified herself as Madeline Bergman and explained what was going on. The BOTTLE SHIP scientists were trying to create a special forces unit modeled after the Space Pirates, which was then succeeded by cloning Metroids off fragments of the Baby on Samus' suit. An AI that recreated Mother Brain's thought processes so that the Metroids could be controlled was also developed, and nicknamed MB. Madeline gives Samus the directions to Sector Zero, a secret area on the BOTTLE SHIP containing the Metroids and MB. Samus set off to destroy them, however, Adam raced off to stop her. Samus walked to the entrance and was suddenly shot when about to kill a Metroid, being weakened by Adam so that she couldn't strongarm her way past him. He gave her his last orders and proceeded to detach and destroy Sector Zero. Samus mourned his death, but eventually recovered and swore to finish the mission.

Samus is forced to fight another Queen Metroid.

Returning to the Bioweapon Research Center to locate a survivor and find and defeat Ridley, she found the latter reduced to a dried husk, and later came across several hatched Metroid Eggs. Samus is then attacked by a Queen Metroid, who spawns Metroids as Samus engages it once again. Samus then chased the survivor, who also identifies herself as Madeline Bergman. Madeline cleared up Samus' confusion: she had actually met MB earlier. MB then stepped in and aimed a Freeze Gun at the two of them before numerous Federation Marines invaded and froze her. She then summoned an army of Ghalmanians, Mighty Griptians and Desbrachians to attack, but is ultimately killed by the Marines. As Madeline mourns, The Colonel steps in and praises Samus' work during the mission, but states that she is now an outsider due to the death of everyone in the platoon, and thus she cannot have any contact with Madeline. However, it turns out that Anthony survived his encounter with Ridley by freezing a Magdollite, revealed when he volunteers to escort Samus back to her ship. Leaving the BOTTLE SHIP with the two of them, Samus reflected on Adam and MB as she flew towards Galactic Federation Headquarters.

Samus shares a last, tender moment on the BOTTLE SHIP with Adam's helmet.

Several days later, the Federation decided to destroy the BOTTLE SHIP. Samus returned, however, to recover an important item. Progressing through the environments once again, and defeating her old foe Phantoon, she eventually reached Adam's post, finding his abandoned helmet. Embracing it, Samus reverted to her Zero Suit, and held the helmet as she raced to her gunship.

SR388 was now free of Metroids, and so the Galactic Federation decided to send in a research party to investigate the planet. Due to her previous experience with the planet and its inhabitants, Samus was hired to serve as a guide to the researchers, to collect samples of life for the Biologic Space Laboratories research station. The researchers and Samus arrived on the planet, and when they were trying to capture a Hornoad, a mysterious organism injected itself inside Samus. Thinking nothing of it, the team continued on their mission. After their search was completed and the team returned to their ships, the parasite, which had infested Samus' central nervous system, caused her to fall unconscious. Though her gunship crashed into an Asteroid belt, Samus was safely ejected from the ship and her escape pod was retrieved by the BSL. She was far from safe, however, as the parasites (which would later be named X) continued to spread throughout her body.

The X had infected so much of Samus' Power Suit that large portions of it had to be surgically removed, drastically altering its physical appearance. She was initially given a less than 1% chance of survival, but fortunately the scientists discovered a cure: Metroid DNA. The Metroids were discovered to have been created by the Chozo in order to control the X. With this knowledge in mind, the scientists used a culture of Metroid cells extracted from the Baby to make a vaccine. The vaccine was an astonishing success; the X were completely purged from Samus' body, curing her completely. However, it also had some unexpected side effects: Now that she was immune to the X, Samus could absorb them to regain energy and Missiles. She also gained the Metroid’s trademark weakness to cold. More than just her biology changed, however; the surgical removal of parts of her Power Suit had left her with a radically different appearance: the new Fusion Suit. She then recalled that, before that point, the Baby had saved her twice, once against Ridley on SR388 and the other time against Mother Brain on Zebes.

Despite her recent illness, Samus was not given furlough by the Federation. She was immediately issued a new Gunship with an onboard computer to serve as an aide. This computer’s personality reminded her heavily of her former Commanding Officer and so, with irony noted, she chose to name it Adam in his memory. Samus was then sent to the BSL research station where the last batch of creatures from SR388 and the infected parts of her Power Suit were sent. She was to investigate an unexplained explosion in the Quarantine Bay. To her great surprise, she discovered that the X Parasite within her Suit had taken on her form, and it had become the SA-X (short for Samus Aran-X). It was responsible for the breach of Quarantine Bay, and as a result, the X ran amok throughout the station. All the researchers aboard the station were dead, and it was up to Samus to contain this breach. The X and the SA-X made many attempts to kill her, but Samus was always able to outsmart them, even in her weakened state.

Samus and the SA-X in the Restricted Lab.

Eventually, Samus’s missions through the BSL brought her to the Restricted Lab. After acquiring the Wave Beam, Samus was able to bypass the security door and enter inside. Inside the lab, Samus made a surprising discovery: the Galactic Federation were cloning Metroids. Before she could investigate further, she found the SA-X had followed her inside the lab and was releasing the Metroids so it could attack them. The Metroids soon overpowered it, but the SA-X’s breakout had set off the lab’s self-destruct failsafes. Samus managed to escape, but the lab broke away from the rest of the station and exploded, destroying the Metroids and the SA-X together.

When Samus spoke again to Adam, he was angry with her for meddling in top-secret Federation research. He also informed her that the Federation was very interested in his extensive research on the X and viewed it as a wonderful organism with a variety of uses. Several Federation officials were coming to the BSL in hopes of capturing the X and SA-X (due to asexual reproduction, there were now no fewer than ten SA-X aboard the station) for military purposes. Samus vocally disapproved, insisting that the Federation were underestimating the threat that the X posed, and resolved to activate the ship's self-destruct to destroy the X, and herself if necessary.

Adam converses with Samus.

Adam was aware of this, though, and thus locked all the doors. Samus reacted with outrage when she discovered what it had done and angrily yelled, “Don’t let them do this! Can’t you see what will happen, Adam?” The computer was confused at this response, as Samus had never disclosed her personal nickname for it. It asked for an explanation as to who this Adam was. Samus only told him that Adam was a friend who understood when sacrifices had to be made. From this, the computer was able to correctly deduce that Adam had given up his life to save Samus. However, it disregarded this, since Samus was incorrectly assuming that destroying the station would defeat the X for good, and curtly decided: “When Adam chose who would live, he chose the wrong person.”

Suddenly, something unusual began happening. The computer began adopting the persona of the former Adam. It unlocked the doors and told Samus that her instructions were to head to the Navigation Deck and change the station’s orbit so that it would crash into SR388, so that when it self-destructed, the planet too would be caught in the field. It ended this sudden command with Adam’s famous clincher: “Any objections, lady?”

Samus and the SA-X duel the Omega Metroid.

Refreshed with a new spirit, Samus headed to the Navigation Deck, but the SA-X burst in once more with murder on its mind. Endowed with her new weapons, Samus managed to defeat the clone, continuing fearlessly even when it mutated into a massive beast and then into a Core-X. Eventually, the SA-X was reduced once more to a lowly X, but before Samus could absorb it, it eluded her and escaped into the ventilation system. Disappointed and tired, but still determined, Samus continued her way up the Navigation Deck until she reached the terminal that controlled the station’s orbit. Samus altered its orbit and set off the self-destruct, then proceeded to return to the Docking Bay. When she arrived, though, her ship was nowhere to be found, and she was suddenly ambushed by an Omega Metroid, the evolved form of a Metroid that had escaped the Restricted Lab before its destruction. The creature defeated her in a single blow, but just before it could kill her, the SA-X appeared and began attacking the Metroid with its Ice Beam. The Omega Metroid recovered in time and attacked the SA-X, giving Samus enough time to absorb her doppelganger. Endowed with her Ice Beam once more, Samus made short work of the Omega Metroid. Shortly after killing it, her ship then returned to the station to save her. Samus flew away just before BSL, and SR388, exploded together.

Back in the safety of space, Samus discovered that it is a common practice for the Federation to upload the minds of great leaders to computers and that this is what had happened to Adam. After this point, it is unknown what will happen to Samus, as she disobeyed a direct order from the Federation, and subsequently destroyed all their research aboard the BSL.

"What's the matter? All I said was that Komaytos look like little Metr—" Non-canon warning: This article or section contains information that may not be considered an official part of the Metroid series in the overall storyline by Nintendo.

During an unknown period of time, Mother Brain inhabited an asteroid called Metroid, and was approached by a bounty hunter named 'Big Time' Brannigan, who convinced her to hire him because of his 100% efficiency rating. Mother Brain tasked him with locating and terminating an intruder (Samus) on Metroid. Samus was in the process of invading the facility, fighting through waves of enemies when Big Time appeared and challenged her. He caused her to fall on top of him, and the two recognized each other. Samus, unaware that he was sent to capture her, suddenly found herself ambushed when a plethora of enemies appeared to back Brannigan. She quickly booby trapped her hand gun behind her back and surrendered herself to him. The pair reached Mother Brain's chamber, where said person told him he could pick up his pay on the way out. 'Big Time', however, was urged to kill Samus to make him the top bounty hunter undisputed, but as he tried to shoot her, the gun exploded. An enraged Mother Brain orders that he be fed to the Metroids, while Samus leaves, remarking that Big Time did get her, but not the way he wanted.

Some time after the defeat of Mother Brain (presumably after Super Metroid), an invasion of the Messina system took place, organized by a group of Chozo known as the "True Chozo". Samus was a victim of their random starship attacks, and she crash-landed on the Tranquility Base airfield, where she was put into rehabilitation. At the end of the story, she explained to Armstrong Houston that she was "supposed to get ready to go out and save the universe again," but it "looks like [she] had nothing to worry about."

At an unknown point in time years after the Zero Mission, Samus responded to a distress call originating from a frontier planet called Liberty. She found that its small village was under Space Pirate attack, and she took her enemies by storm, much to the fascination of a young, reckless boy named Joey Apronika. As she was preparing to leave, Joey pursued Samus in the hopes of accompanying her. She refused and quickly became annoyed with his rampant behavior, although she was forced to save him when they were attacked by Doruba. Samus became reluctant to fire a Super Missile at the beast, because Joey would have been caught in the blast, although he encouraged her to do so.

The pair survived the blast, although Samus ordered Joey to return to the village immediately. He objected, because the two of them had defeated Doruba together. Samus explained that although Doruba might not have posed a challenge, the creature that she was hunting, Dragüd, possessed a life form that is a challenge, and a very deadly one at that: the Metroid. Samus told him the story of her Zero Mission and left. Whilst she ran off to fight Dragüd, Joey followed her in secret using the guise of a molten Pirate skin and pretended that he was going to see the Megaroid, a Metroid created by Dragüd from dead Metroid cells.

The creature escaped containment and quickly began consuming the energy of all Pirates, and the ship itself. It grew into an enormous creature that Samus found was not affected by her favorite tactic of Ice Beam and Missile fire used in tandem. The creature split into numerous crystals that multiplied into living creatures and engulfed Samus before moving on to the Liberty village. Joey collected several Space Torches and used them to lead the Megaroids away while Samus destroyed the Megaroids engulfing her using her Plasma Beam and Ice Beam in tandem to create thermal shock. She then pursued Joey to Mount Pagos, a long inactive volcano that she reactivated with a Power Bomb and Super Missile, which obliterated the Megaroids.

Samus then announced that she was returning to space. A while later, Joey sat at his father's grave and discovered a buried parcel in it, containing his old armor: the Field Knuckle. Samus saw potential in Joey, and promised to take him as far as a large space station where a friend of hers lived. She dropped him off at an engine shop, the Junk Quixote, run by her acquaintance Diesel. The pair found Jealousy, another Space Pirate, instead. He was holding Diesel hostage. The creature summoned his bodyguard, Bomad, to fight Samus. Joey rescued Diesel and fought off Jealousy's Pirates using his Field Knuckle, until Bomad unleashed a gravity bomb that obliterated everything in the room except Bomad himself, Samus, Joey and Diesel. Samus finished Bomad off. Diesel was released, and his first order of business for Joey was to fix the shop.

Some time later, Samus discovers that the Special Forces Ship Otowa disappeared. She tracks it to Degrade, a planet she soon finds has magnetic storms that damage her ship and render her unable to leave (echoing Aether). Samus discovers the ship with only a fraction of its passengers alive, being attacked by Giants. Samus destroys much of the behemoths, but one prepares to eat one of the survivors, Dr. Diana Apronika, Joey's mother. Joey, who has come searching for his mother kills this Giant, saving her. The remainder of the Giants flee, as another creature swarms in the background.

These creatures, Amoks, turn out to resemble large penguins. The survivors stated that these creatures ate a large fraction of their crew. The Amoks then turn on the survivors, but Samus helps them to repel the attack. Samus and Diesel make a plan to use a crashed ship they saw to escape with the Otowa survivors. Two days later, Samus asks Joey about his mother. Joey feels that he is always in her way and that she prioritizes her work. Samus confesses that she envies Joey for being able to grow up with his parents. The Amoks return and charge at the survivors, but Samus holds them off with a Power Bomb.

Diesel discovers a damaged but still functional KI-1 Class Ship, which they hope to use to escape. Inside, Joey discovers a nest of eggs and the mother of the Amoks. Samus finds that her beams have no effect on the creature, and she cannot use her Super Missiles or Power Bombs due to her proximity to the ship, but Joey is able to hold the creature off with his Field Knuckle. As the ship takes off, Samus uses a Super Missile and destroys the creature. The Amoks feed on the corpse, off-screen, as Samus, Joey, Diesel and the Otowa survivors escape in the Junk Hawk and KI-1 ship (towing Samus' ship).

Following the excursion at Degrade, Samus destroys Bioroid Delta III, a combat bioroid that destroyed a ship en-route to a demolition site, and Dangelo, an escaped convict from her past who launches terrorist attacks wearing a Power Suit resembling hers. Joey and Diesel are kidnapped by the Dominion, a paramilitary organization that sells weapons of mass destruction. Samus rescues them and they help her to fight through the Dominion's base on the Demon Planet, destroying several mechanisms modeled after Samus. The Dominion is dealt a destructive blow and Samus is congratulated for her efforts in exposing their existence. Samus is later lured into a trap upon receiving a call from Joey, and then sealed into an Ability Disassembly and Conversion Device, which torturously downgrades her Power Suit and extracts seven of her most important abilities. Joey sacrifices himself to stop Samus from dying. By this point, Samus has accepted Joey as a partner and her anger allows her to easily kill the Body Snatcher, the being that took her powers. Samus is then ambushed by Greed, a dragon-like being resembling Ridley, who takes off for space and challenges her to follow him.

Samus, with Joey and Diesel as company, pursues Greed to the Extreme Galaxy, a lawless sector outside of the Galactic Federation's control. The trio are thrust into numerous dangerous and often physics-defying situations to recover her stolen abilities from Greed's gang, the Greed Corps, and six of his henchmen, the Deadly Six Stars. Samus succeeds in recovering most of her abilities, but after triggering a volcano to kill the last Star, Defen, she lost the Data Capsule containing her Varia Suit.

The trio later discover Greed's real plan: to avenge the destruction of his race, which includes Ridley, that had led the Space Pirates for generations, and to access a destructive power in the ancient ruins on a diamond-shaped planet. Samus is captured and brought to the ruins, where her body is used to allow Greed to obtain the power. While she lies unconscious in the Hall of the Gods, Joey, Diesel and the defecting Greed Corps general Knight battle the other general, Bishop, who wants the power for himself. Bishop reveals that he recovered the Varia Suit from the ocean world, as well as Samus's Plasma Beam. After a bloody skirmish, Bishop is killed and the Capsules join with Samus to revive her and fully restore her abilities. Shortly after this, a black hole is created in space, which begins to impact the entire universe.

Samus, prepared to battle Greed, instructs Joey and Diesel to leave. As they protest, she explains that she heard the voice of an animus dwelling in the ruins, who explained that those who access the power must make a choice between the power of the past or the future. Her hearing this animus makes her the only person who can challenge Greed. Before entering the door, she reveals her true identity to Joey by removing her Power Suit, and promises him that he will rise to do battle in the future. She then rematerializes her Power Suit and storms off to confront Greed.

Inside, Samus discovers Greed suffering a "pathetic" death - he chose the power of the future and is being swallowed by that power. The animus prepares to destroy the universe until Samus points out that she has not made a choice. Rather than choosing the past or the future, she chooses the present. The animus, content with her decision, produces a white light. As Samus touches it, a white hole is produced in space, counteracting the black hole and restoring power to the universe. What becomes of Samus is unclear, but it is likely she left the ruins to continue bounty hunting, although she and Joey have gone their separate ways.

“

Surprised that I'm a woman?

Although I am a woman, from the time I was very young, I have carried the destiny of a warrior on her back, like a mother carries her child, even though I have never given birth or raised one. But by fighting, I have been able to protect and nurture children, who are our hope for the future...

I do not intend to die! I am still needed to provide hope, to provide peace. But this battle is mine to fight!

In the future, you will become a fine warrior... and when the time comes to protect everyone else's future, then it will be your turn to fight, Joey!

Become strong, Joey! Grow into a strong, kind man... for whatever hard times may come.

And so I will not lose sight of my goals and purpose. I will not forget you!